rs9904838

Positions:

• chr17-55968960-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653862.1(ANKFN1):​c.208+3284A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 151,928 control chromosomes in the GnomAD database, including 2,386 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (2386 hom., cov: 31)
• Consequence: ANKFN1 ENST00000653862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

ANKFN1 (HGNC:26766): (ankyrin repeat and fibronectin type III domain containing 1) Predicted to be involved in establishment of mitotic spindle orientation and regulation of establishment of bipolar cell polarity. Predicted to act upstream of or within behavioral fear response; equilibrioception; and locomotor rhythm. Predicted to be active in spindle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKFN1	ENST00000635860.2	c.34+3284A>G		intron_variant		5		ENSP00000489811	A2
ANKFN1	ENST00000653862.1	c.208+3284A>G		intron_variant				ENSP00000499705	A2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19101 AN: 151810 Hom.: 2358 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.111

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.126 AC: 19175 AN: 151928 Hom.: 2386 Cov.: 31 AF XY: 0.126 AC XY: 9340 AN XY: 74260

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.0762

Gnomad4 ASJ AF: 0.0695

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0269

Gnomad4 NFE AF: 0.0375

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0543 Hom.: 730

Bravo AF: 0.136

Asia WGS AF: 0.170 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.029
DANN	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9904838; hg19: chr17-54046321;